Bismark report for: /gscratch/srlab/sr320/data/cvirg/39F_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/39F_R2_val_2.fq.gz (version: v0.22.3)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cvirg-genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	156641108
Number of paired-end alignments with a unique best hit:	88891085
Mapping efficiency:	56.7% 
Sequence pairs with no alignments under any condition:	44785775
Sequence pairs did not map uniquely:	22964248
Sequence pairs which were discarded because genomic sequence could not be extracted:	1498

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	22395048	((converted) top strand)
GA/CT/CT:	22304123	(complementary to (converted) top strand)
GA/CT/GA:	22052360	(complementary to (converted) bottom strand)
CT/GA/GA:	22138056	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3682137464

Total methylated C's in CpG context:	57008069
Total methylated C's in CHG context:	2722172
Total methylated C's in CHH context:	11308743
Total methylated C's in Unknown context:	285118

Total unmethylated C's in CpG context:	420738828
Total unmethylated C's in CHG context:	650131464
Total unmethylated C's in CHH context:	2540228188
Total unmethylated C's in Unknown context:	11828259

C methylated in CpG context:	11.9%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.4%
C methylated in unknown context (CN or CHN):	2.4%


Bismark completed in 0d 15h 21m 45s